Another vote for WAP. My family has membership to SD Zoo which includes WAP and we rarely visit the zoo. We were just at WAP about 1-1/2 weeks ago on a Friday (low crowds) and it gets better every time. The exhibits are good. The Lion Camp is awesome-be sure to check it out early in the day, or just before closing, especially if it's hot. Also the gorillas.
The problem with the zoo is, IMO, the exhibits look much less natural. And, don't be fooled, it can get almost as hot at the zoo as at WAP. If you're going in the evening either to the zoo or WAP (offered during the summer) you should know that there a very few lights on the exhibits. You really can't see many animals after dark-though it is cooler.
Have fun!